Syllabus for Fall 2017
Course OutlineThis course is an introduction to the field of molecular systems biology, which aims to understand the mechanisms underlying complex biological processes. Key to this endeavor is the process of formulating and analyzing mathematical models. In this course, we will learn how to relate mechanistic insights gleaned from data to cartoon drawings of the system, then how to translate the cartoon drawing into mathematical expressions, next how to use optimization techniques to fit any unknown parameters, and finally how to analyze models by simulating biological experiments and assessing sensitivity to perturbation.
- Formulating models using standard kinetics (what math to use)
- Motifs in biological systems (understanding common pieces of models)
- Simulation techniques (how to solve ODE's with a computer)
- Parameter-fitting through optimization (finding parameter values that minimize our error)
- Sensitivity analysis (assessing how a model reacts to changes in parameters)
The course grade will be determined as follows:
Homework and ProjectsThere are two types of work you need to do outside of class: (1) homework assignments which help you learn new material (by reading or trying out some new code), and (2) projects, which give you the opportunity to study a topic in depth. On most days there will be both a project and a homework due at some point in the future. Please plan accordingly. You will need to balance both types of work for this course. In general, homework assignments are meant to give you additional practice with coding and reading journal articles. Approximately twice in the semester, you will be given the responsibility of presenting one or more figures in a journal article. Grading for the homework assignments will be essentially boolean. As long as you turn in a complete set of answers and demonstrate (with the quality of the answer) that you put your best effort into them, you will receive full credit. Late or incomplete homeworks will have points deducted. Projects are meant to be more polished and will be graded with greater attention to detail (see below).
Homework AssignmentsFor most class meetings, there will be an assignment to help you to prepare for the meeting. Most days, this will include reading one or more journal articles and answering questions about them. Approximately twice in the semester, it will also involve preparing to present the content of a figure in the article (i.e. explaining to your classmates what was done to generate the data for the figure, how to read the figure, and what conclusions can be drawn from the results). Some days, it will mean writing some Matlab code. A note about the readings: Instead of using a textbook for this course, we are going straight to the source, and will be reading journal articles. To help you make the most this experience, all readings will be accompanied by a set of questions. The questions are designed to help you get the most out of the paper.
ProjectsThere will be one project for each topic in covered in the course. This means there will be approximately 5 projects, all of which give you the opportunity to explore that topic in depth. For each project, you will implement Matlab programs, analyze results, and write a short document summarizing and analyzing your methods and results. A set of questions will provide the framework for your code-writing and analysis. Because I want you to have the chance to engage deeply and to have some intellectual autonomy, these questions are intentionally open-ended and there will not be a detailed set of instructions.
The write-ups should be neat and thorough, yet succinct. Answering all of the questions adequately will earn you a B+. To earn an A- or A, you must be particularly convincing and thorough when you answer the "why?" or "how?" or "what if?" questions. This does not mean that I want you to turn in reams of paper. It means that you should include carefully chosen additional examples or evidence to back up your point. The questions I will be asking myself when I am grading are, for example: Does this make sense? Does she make it clear why she came to her conclusions? Is he being precise? Does he include the appropriate mathematics when they are called for? Is her intuition grounded in a solid understanding of the material? Projects are graded on a 30 point scale. Here is a rough guide to grading:
|Answers are well-written, show depth of understanding, and include appropriate figures. Additional code or simulations are used to back up points.||30|
|Answers are well-written, show some depth of understanding, and include appropriate figures. There may be a small amount of additional code or simulations used to back up points.||28|
|Answers are well-written, show some depth of understanding, and include appropriate figures. No extra work was done.||26|
|Answers are understandable, show some understanding, and include appropriate figures. No extra work was done.||25|
Late Policy: If a project is turned in more than 1 day late, then you can earn only 26 out of 30 points. This policy is intended to encourage you to keep moving forward and not to spend lots of time on an early project when you should be moving forward.
Class ParticipationYou are expected to attend every class. Some class meetings will involve hands-on lessons difficult to make up. Other class meetings will involve discussion, which is a vital part of the learning experience and we cannot have good discussion without you! Class participation is so important that 5% of your grade depends upon your participation.
Office HoursPlease visit me in my office! During office hours, I will of course be available. Outside of office ours, I will often be in my office with the door open. Please come in! If you want to be sure I will be there, just ask me in person or send me an email. I will do my best to be there.
Collaboration and Academic Honesty
Computer science, both academically and professionally, is a collaborative discipline. In any collaboration, however, all parties are expected to make their own contributions and to generously credit the contributions of others. In our class, therefore, collaboration on homework and programming assignments is encouraged, but you as an individual are responsible for understanding all the material in the assignment and doing your own work. Always strive to do your best, give generous credit to others, start early, and seek help early from both your professors and classmates.
The following rules are intended to help you get the most out of your education and to clarify the line between honest and dishonest work. We reserve the right to ask you to verbally explain the reasoning behind any answer or code that you turn in and to modify your project grade based on your answers. It is vitally important that you turn in work that is your own. We do use automated plagiarism detection software, so please be sure to abide by these, rather minimal, rules. Reports of academic dishonesty are handled by an academic review board and a finding of academic dishonesty may result in significant sanctions. For more details on Colby's Academic Integrity policies and procedures, see colby.edu/academicintegrity.
- If you have had a substantive discussion of any programming project with a classmate, then be sure to cite them in your write-up. If you are unsure of what constitutes "substantive", then ask me or err on the side of caution. As one rule of thumb, if you see more than 10 lines of someone else's code, then you should cite them. You will not be penalized for working together.
You must not copy answers or code from another student either by hand or electronically. Another way to think about it is that you should be talking English with one another, not Matlab.
Sexual Misconduct/Title IX Statement
Colby College prohibits and will not tolerate sexual misconduct or gender-based discrimination of any kind. Colby is legally obligated to investigate sexual misconduct (including, but not limited to sexual assault and sexual harassment).
If you wish to speak confidentially about an incident of sexual misconduct, please contact Colby Counseling Services (207-859-4490) or the Director of the Gender and Sexual Diversity Program, Emily Schusterbauer (207-859-4093).
Students should be aware that faculty members are considered responsible employees; as such, if you disclose an incident of sexual misconduct to a faculty member, they have an obligation to report it to Colby’s Title IX Coordinator. “Disclosure” may include communication in-person, via email/phone/text, or through class assignments.
To learn more about sexual misconduct or report an incident, visit http://www.colby.edu/sexualviolence/.